Create kinetics dataset for a list of peptides and their states
create_kinetic_dataset.RdGenerates the data set of deuterium uptake between selected time points based on supplied peptide list.
Arguments
- dat
dat data imported by the
read_hdxfunction.- peptide_list
list of peptides for the calculation.
- protein
chosen protein.
- time_0
minimal exchange control time point of measurement.
- time_100
maximal exchange control time point of measurement.
- deut_part
deuterium percentage in solution used in experiment, value from range [0, 1].
Value
a data.frame object.
Details
This is a wrapper for calculate_kinetics, but for
the peptide list instead of one peptide.
Examples
dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv"))
#> [1] ""
peptide_list <- data.frame(Sequence = c("INITSSASQEGTRLN", "INITSSASQEGTRLN"),
state = c("CD160", "CD160_HVEM"),
start = c(1, 1), end = c(15, 15))
create_kinetic_dataset(dat, peptide_list)
#> Protein Sequence Start End State time_chosen Exposure
#> 1 db_CD160 INITSSASQEGTRLN 1 15 CD160 0.001 0.001
#> 2 db_CD160 INITSSASQEGTRLN 1 15 CD160 0.167 0.167
#> 3 db_CD160 INITSSASQEGTRLN 1 15 CD160 1.000 1.000
#> 4 db_CD160 INITSSASQEGTRLN 1 15 CD160 5.000 5.000
#> 5 db_CD160 INITSSASQEGTRLN 1 15 CD160 25.000 25.000
#> 6 db_CD160 INITSSASQEGTRLN 1 15 CD160 120.000 120.000
#> 7 db_CD160 INITSSASQEGTRLN 1 15 CD160_HVEM 0.001 0.001
#> 8 db_CD160 INITSSASQEGTRLN 1 15 CD160_HVEM 0.167 0.167
#> 9 db_CD160 INITSSASQEGTRLN 1 15 CD160_HVEM 1.000 1.000
#> 10 db_CD160 INITSSASQEGTRLN 1 15 CD160_HVEM 5.000 5.000
#> 11 db_CD160 INITSSASQEGTRLN 1 15 CD160_HVEM 25.000 25.000
#> 12 db_CD160 INITSSASQEGTRLN 1 15 CD160_HVEM 120.000 120.000
#> Modification frac_deut_uptake err_frac_deut_uptake deut_uptake
#> 1 NA 0.3693522 0.00129470 0.03860574
#> 2 NA 76.9416288 0.38198929 8.04215607
#> 3 NA 84.2545964 0.60898022 8.80652807
#> 4 NA 87.5793488 0.59219322 9.15404057
#> 5 NA 93.2210067 0.57651483 9.74372257
#> 6 NA 95.5203706 0.83024122 9.98405857
#> 7 NA 0.3721661 0.00283752 0.03860574
#> 8 NA 74.4538227 0.66707227 7.72328457
#> 9 NA 81.6064285 0.98612947 8.46524257
#> 10 NA 82.9536479 0.87902224 8.60499307
#> 11 NA 87.7240119 0.70630534 9.09983507
#> 12 NA 95.2046776 0.78903153 9.87582357
#> err_deut_uptake theo_frac_deut_uptake err_theo_frac_deut_uptake
#> 1 0.00000000 -0.4493436 0.0000000
#> 2 0.02827429 62.6120329 0.2227781
#> 3 0.05566577 68.6346539 0.4386003
#> 4 0.05293102 71.3727658 0.4170528
#> 5 0.04964457 76.0189737 0.3911582
#> 6 0.07940910 77.9126232 0.6256782
#> 7 0.00000000 -0.4493436 0.0000000
#> 8 0.03634286 60.0995884 0.2863518
#> 9 0.07936215 65.9456056 0.6253083
#> 10 0.06332496 67.0467243 0.4989484
#> 11 0.02354604 70.9456712 0.1855234
#> 12 0.03208667 77.0598207 0.2528165
#> theo_deut_uptake err_theo_deut_uptake Med_Sequence
#> 1 -0.05702927 0.00000000 8
#> 2 7.94652106 0.02827429 8
#> 3 8.71089306 0.05566577 8
#> 4 9.05840556 0.05293102 8
#> 5 9.64808756 0.04964457 8
#> 6 9.88842356 0.07940910 8
#> 7 -0.05702927 0.00000000 8
#> 8 7.62764956 0.03634286 8
#> 9 8.36960756 0.07936215 8
#> 10 8.50935806 0.06332496 8
#> 11 9.00420006 0.02354604 8
#> 12 9.78018856 0.03208667 8
peptide_list2 <- data.frame(Sequence = c("INITSSASQEGTRLN", "LICTVW"),
state = c("CD160", "CD160"),
start = c(1, 16), end = c(15, 21))
create_kinetic_dataset(dat, peptide_list2)
#> Protein Sequence Start End State time_chosen Exposure Modification
#> 1 db_CD160 INITSSASQEGTRLN 1 15 CD160 0.001 0.001 NA
#> 2 db_CD160 INITSSASQEGTRLN 1 15 CD160 0.167 0.167 NA
#> 3 db_CD160 INITSSASQEGTRLN 1 15 CD160 1.000 1.000 NA
#> 4 db_CD160 INITSSASQEGTRLN 1 15 CD160 5.000 5.000 NA
#> 5 db_CD160 INITSSASQEGTRLN 1 15 CD160 25.000 25.000 NA
#> 6 db_CD160 INITSSASQEGTRLN 1 15 CD160 120.000 120.000 NA
#> 7 db_CD160 LICTVW 16 21 CD160 0.001 0.001 NA
#> 8 db_CD160 LICTVW 16 21 CD160 0.167 0.167 NA
#> 9 db_CD160 LICTVW 16 21 CD160 1.000 1.000 NA
#> 10 db_CD160 LICTVW 16 21 CD160 5.000 5.000 NA
#> 11 db_CD160 LICTVW 16 21 CD160 25.000 25.000 NA
#> 12 db_CD160 LICTVW 16 21 CD160 120.000 120.000 NA
#> frac_deut_uptake err_frac_deut_uptake deut_uptake err_deut_uptake
#> 1 0.36935223 0.001294700 0.038605737 0.00000000
#> 2 76.94162879 0.381989286 8.042156070 0.02827429
#> 3 84.25459637 0.608980217 8.806528070 0.05566577
#> 4 87.57934878 0.592193216 9.154040570 0.05293102
#> 5 93.22100671 0.576514834 9.743722570 0.04964457
#> 6 95.52037061 0.830241218 9.984058570 0.07940910
#> 7 0.03033506 0.000148162 0.000888387 0.00000000
#> 8 25.77526288 1.270721219 0.754849637 0.03703103
#> 9 32.01227510 1.521507750 0.937505637 0.04432270
#> 10 41.67132775 0.581339743 1.220378887 0.01594750
#> 11 49.66438624 1.012471575 1.454462137 0.02878750
#> 12 65.03177370 0.941903476 1.904508637 0.02596870
#> theo_frac_deut_uptake err_theo_frac_deut_uptake theo_deut_uptake
#> 1 -0.4493436 0.0000000 -0.05702927
#> 2 62.6120329 0.2227781 7.94652106
#> 3 68.6346539 0.4386003 8.71089306
#> 4 71.3727658 0.4170528 9.05840556
#> 5 76.0189737 0.3911582 9.64808756
#> 6 77.9126232 0.6256782 9.88842356
#> 7 -10.9156277 0.0000000 -0.49477747
#> 8 5.7180325 0.8169672 0.25918378
#> 9 9.7477327 0.9778337 0.44183978
#> 10 15.9883949 0.3518288 0.72471303
#> 11 21.1526673 0.6351010 0.95879628
#> 12 31.0814541 0.5729134 1.40884278
#> err_theo_deut_uptake Med_Sequence
#> 1 0.00000000 8.0
#> 2 0.02827429 8.0
#> 3 0.05566577 8.0
#> 4 0.05293102 8.0
#> 5 0.04964457 8.0
#> 6 0.07940910 8.0
#> 7 0.00000000 18.5
#> 8 0.03703103 18.5
#> 9 0.04432270 18.5
#> 10 0.01594750 18.5
#> 11 0.02878750 18.5
#> 12 0.02596870 18.5